Literature DB >> 25619997

Cooperative development of logical modelling standards and tools with CoLoMoTo.

Aurélien Naldi1, Pedro T Monteiro2, Christoph Müssel1, Hans A Kestler3, Denis Thieffry1, Ioannis Xenarios2, Julio Saez-Rodriguez1, Tomas Helikar1, Claudine Chaouiya1.   

Abstract

The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour and provide (testable) predictions by performing in silico experiments. In this context, qualitative, logical frameworks have emerged as relevant approaches, as demonstrated by a growing number of published models, along with new methodologies and software tools. This productive activity now requires a concerted effort to ensure model reusability and interoperability between tools. Following an outline of the logical modelling framework, we present the most important achievements of the Consortium for Logical Models and Tools, along with future objectives. Our aim is to advertise this open community, which welcomes contributions from all researchers interested in logical modelling or in related mathematical and computational developments.
© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Mesh:

Year:  2015        PMID: 25619997     DOI: 10.1093/bioinformatics/btv013

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  33 in total

Review 1.  Boolean network modeling in systems pharmacology.

Authors:  Peter Bloomingdale; Van Anh Nguyen; Jin Niu; Donald E Mager
Journal:  J Pharmacokinet Pharmacodyn       Date:  2018-01-06       Impact factor: 2.745

2.  Representing dynamic biological networks with multi-scale probabilistic models.

Authors:  Alexander Groß; Barbara Kracher; Johann M Kraus; Silke D Kühlwein; Astrid S Pfister; Sebastian Wiese; Katrin Luckert; Oliver Pötz; Thomas Joos; Dries Van Daele; Luc De Raedt; Michael Kühl; Hans A Kestler
Journal:  Commun Biol       Date:  2019-01-17

3.  Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.

Authors:  Anna Niarakis; Martin Kuiper; Marek Ostaszewski; Rahuman S Malik Sheriff; Cristina Casals-Casas; Denis Thieffry; Tom C Freeman; Paul Thomas; Vasundra Touré; Vincent Noël; Gautier Stoll; Julio Saez-Rodriguez; Aurélien Naldi; Eugenia Oshurko; Ioannis Xenarios; Sylvain Soliman; Claudine Chaouiya; Tomáš Helikar; Laurence Calzone
Journal:  Brief Bioinform       Date:  2021-03-22       Impact factor: 11.622

4.  ASP-based method for the enumeration of attractors in non-deterministic synchronous and asynchronous multi-valued networks.

Authors:  Emna Ben Abdallah; Maxime Folschette; Olivier Roux; Morgan Magnin
Journal:  Algorithms Mol Biol       Date:  2017-08-15       Impact factor: 1.405

5.  The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.

Authors:  Aurélien Naldi; Céline Hernandez; Nicolas Levy; Gautier Stoll; Pedro T Monteiro; Claudine Chaouiya; Tomáš Helikar; Andrei Zinovyev; Laurence Calzone; Sarah Cohen-Boulakia; Denis Thieffry; Loïc Paulevé
Journal:  Front Physiol       Date:  2018-06-19       Impact factor: 4.566

Review 6.  Boolean modelling as a logic-based dynamic approach in systems medicine.

Authors:  Ahmed Abdelmonem Hemedan; Anna Niarakis; Reinhard Schneider; Marek Ostaszewski
Journal:  Comput Struct Biotechnol J       Date:  2022-06-17       Impact factor: 6.155

7.  Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Authors:  Anna Niarakis; Dagmar Waltemath; James Glazier; Falk Schreiber; Sarah M Keating; David Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomáš Helikar; Sylvain Soliman; Laurence Calzone
Journal:  Brief Bioinform       Date:  2022-07-18       Impact factor: 13.994

8.  On the feasibility of dynamical analysis of network models of biochemical regulation.

Authors:  Luis M Rocha
Journal:  Bioinformatics       Date:  2022-05-31       Impact factor: 6.931

9.  Discrete Logic Modeling of Cell Signaling Pathways.

Authors:  Nensi Ikonomi; Silke D Werle; Julian D Schwab; Hans A Kestler
Journal:  Methods Mol Biol       Date:  2022

Review 10.  In Silico Logical Modelling to Uncover Cooperative Interactions in Cancer.

Authors:  Gianluca Selvaggio; Claudine Chaouiya; Florence Janody
Journal:  Int J Mol Sci       Date:  2021-05-05       Impact factor: 5.923

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